[gmx-users] Getting a crystal topology file from pdb2gmx

Wed Nov 11 18:13:28 CET 2015

Dear Justin,

Thank you for your prompt reply Justin. I think that is what I was looking for but did not know such command it existed! I have tried your suggestion however another problem occurs :
Opening force field file /shared/ucl/apps/gromacs/5.1.1/intel-2015-update2/share/gromacs/top/oplsaa.ff/atomname2type.n2tThere are 23 name to type translations in file oplsaa.ffGenerating bonds from distances...atom 618Can not find forcefield for atom C6-3 with 3 bondsCan not find forcefield for atom C9-4 with 3 bondsCan not find forcefield for atom C2-7 with 3 bondsCan not find forcefield for atom C1-8 with 3 bondsCan not find forcefield for atom C5-13 with 3 bondsCan not find forcefield for atom C6-20 with 3 bondsCan not find forcefield for atom C9-21 with 3 bondsCan not find forcefield for atom C2-24 with 3 bondsCan not find forcefield for atom C1-25 with 3 bondsCan not find forcefield for atom C5-30 with 3 bonds---------------------------------------------------------------------------------------------------------------------------------------------Can not find forcefield for atom C5-317 with 3 bondsCan not find forcefield for atom N1-322 with 3 bondsCan not find forcefield for atom C12-323 with 4 bondsCan not find forcefield for atom C11-324 with 3 bondsCan not find forcefield for atom C14-327 with 3 bondsCan not find forcefield for atom C6-346 with 3 bondsCan not find forcefield for atom C9-347 with 3 bondsCan not find forcefield for atom C2-350 with 3 bondsCan not find forcefield for atom C1-351 with 3 bondsCan not find forcefield for atom C5-356 with 3 bondsCan not find forcefield for atom N1-361 with 3 bondsCan not find forcefield for atom C12-362 with 4 bondsCan not find forcefield for atom C11-363 with 3 bonds-------------------------------------------------------------------------------------------------------------------------------------------Can not find forcefield for atom Zr2-590 with 0 bondsCan not find forcefield for atom Zr2-591 with 0 bondsCan not find forcefield for atom Zr2-592 with 0 bondsCan not find forcefield for atom Zr2-593 with 0 bondsCan not find forcefield for atom Zr2-594 with 0 bondsCan not find forcefield for atom O3-595 with 0 bondsCan not find forcefield for atom O3-596 with 0 bondsCan not find forcefield for atom O3-597 with 0 bondsCan not find forcefield for atom O3-598 with 0 bondsCan not find forcefield for atom O3-599 with 0 bondsCan not find forcefield for atom O3-600 with 0 bondsCan not find forcefield for atom O3-601 with 0 bondsCan not find forcefield for atom O3-602 with 0 bondsCan not find forcefield for atom O3-603 with 0 bondsCan not find forcefield for atom O3-604 with 0 bondsCan not find forcefield for atom O3-605 with 0 bondsCan not find forcefield for atom O3-606 with 0 bondsCan not find forcefield for atom O3-607 with 0 bondsCan not find forcefield for atom O3-608 with 0 bondsCan not find forcefield for atom O3-609 with 0 bondsCan not find forcefield for atom O3-610 with 0 bondsCan not find forcefield for atom O3-611 with 0 bondsCan not find forcefield for atom O3-612 with 0 bondsCan not find forcefield for atom O3-613 with 0 bondsCan not find forcefield for atom O3-614 with 0 bondsCan not find forcefield for atom O3-615 with 0 bondsCan not find forcefield for atom O3-616 with 0 bondsCan not find forcefield for atom O3-617 with 0 bondsCan not find forcefield for atom O3-618 with 0 bonds
-------------------------------------------------------Program gmx x2top, VERSION 5.1.1Source code file: /dev/shm/tmp.PwtfSrm0uJ/gromacs-5.1.1/src/gromacs/gmxpreprocess/x2top.c, line: 216
Fatal error:Could only find a forcefield type for 420 out of 618 atomsFor more information and tips for troubleshooting, please check the GROMACSwebsite at http://www.gromacs.org/Documentation/Errors

With the co-ordinate I had, I have no problem visualising in gaussian view. So what can I do to fix this? Does that mean I have to write a forcefield and incorporate into GROMACS? I know this sounds very rookie, but what is the format of .n2t and do I put that file in my working directory? Thanks for your help.
Ben

> To: gmx-users at gromacs.org
> From: jalemkul at vt.edu
> Date: Wed, 11 Nov 2015 11:19:46 -0500
> Subject: Re: [gmx-users] Getting a crystal topology file from pdb2gmx
> 
> 
> 
> On 11/11/15 11:05 AM, Ben Tam wrote:
> > Hi Justin,
> >
> > I am using Gaussian with basis set 6-31G* and LanL2DZ to calculate the charges of the structure and using UFF for the lennard jones. When I answered CHARMM27, I am assuming the question was what is the option that was given when I typed 'gmx pdb2gmx'. In all honesty, I have no particular reason for using CHARMM or AMBER. All I want out of it is the atom to atom bonding instead of painstakingly  insert it by manual.
> 
> The reason I ask is that the prerequisite for your work is that you have 
> incorporated all of that into a GROMACS force field (or built a custom one 
> yourself).  pdb2gmx does not work magic.  You need to have everything already 
> laid out in terms of the charges, types, and connectivity already.  A better 
> choice in your case is almost certainly x2top, because pdb2gmx is generally 
> intended for linear polymers with limited branching.  x2top will determine 
> connectivity from distances set in an .n2t file.  I would strongly suggest this 
> for any crystalline material.  The point about a custom force field remains, though.
> 
> -Justin
> 
> > Ben
> >
> >> To: gmx-users at gromacs.org
> >> From: jalemkul at vt.edu
> >> Date: Wed, 11 Nov 2015 10:50:29 -0500
> >> Subject: Re: [gmx-users] Getting a crystal topology file from pdb2gmx
> >>
> >>
> >>
> >> On 11/11/15 10:37 AM, Ben Tam wrote:
> >>> Hi Micholas,
> >>> I am using CHARMM27.
> >>
> >> And, out of curiosity, what is the source of your Zr parameters?
> >>
> >> -Justin
> >>
> >>> Ben
> >>>
> >>>> From: smithmd at ornl.gov
> >>>> To: gmx-users at gromacs.org
> >>>> Date: Wed, 11 Nov 2015 15:26:30 +0000
> >>>> Subject: Re: [gmx-users] Getting a crystal topology file from pdb2gmx
> >>>>
> >>>> Quick clarifying question:
> >>>>
> >>>> What force-field are you trying to use?
> >>>>
> >>>> -Micholas
> >>>>
> >>>> ===================
> >>>> Micholas Dean Smith, PhD.
> >>>> Post-doctoral Research Associate
> >>>> University of Tennessee/Oak Ridge National Laboratory
> >>>> Center for Molecular Biophysics
> >>>>
> >>>> ________________________________________
> >>>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Ben Tam <btam125 at hotmail.co.uk>
> >>>> Sent: Wednesday, November 11, 2015 10:10 AM
> >>>> To: gromacs.org_gmx-users at maillist.sys.kth.se
> >>>> Subject: [gmx-users] Getting a crystal topology file from pdb2gmx
> >>>>
> >>>> Dear Gromacs users and Developer,
> >>>>
> >>>> I am trying to run a simulation for a metal organic frameworks (MOFs), it is a crystallise periodic structure. The original file is in .cif format, however using material studio I converted it to .pdb file. Now I am stuck on converting .pdb file to a topology file in gromacs using 'gmx pdb2gmx'. There is an error when I  try:
> >>>> Residue 'MOL' not found in residue topology database
> >>>> The structure I am simulating contained Zr  atoms, henceforth there are no residues can match that. I know it is a cif file and kind of forcing it into a .pdb file. My question is this, are there better way to convert a crystal structure (.cif file) in gromacs so I can get the topology?
> >>>> Kind regards,
> >>>>
> >>>> Ben
> >>>>
> >>>> --
> >>>> Gromacs Users mailing list
> >>>>
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> >>>>
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> >>>    		 	   		
> >>>
> >>
> >> --
> >> ==================================================
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >>
> >> Department of Pharmaceutical Sciences
> >> School of Pharmacy
> >> Health Sciences Facility II, Room 629
> >> University of Maryland, Baltimore
> >> 20 Penn St.
> >> Baltimore, MD 21201
> >>
> >> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> >> http://mackerell.umaryland.edu/~jalemkul
> >>
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> >   		 	   		
> >
> 
> -- 
> ==================================================
> 
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> 
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> 
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
> 
> ==================================================
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